[R] Calculation of normalised red and green intensities

[Henrik Bengtsson]

Hi, here's the calculations

  M = log2(R/G)     = [log rules] = log2(R)-log2(G)     (1)
  A = 1/2*log2(R*G) = [log rules] = (log2(R)+log2(G))/2 (2)

where log2(x) is the logarithm of x with base 2. If R,G > 0, there is
a one-to-one relationship between (A,M) and (G,R) as follows

  R = (2^(2A+M))^(1/2) = sqrt(2^(2A+M))   (3)
  G = (2^(2A-M))^(1/2) = sqrt(2^(2A-M))   (4)

It's a good exercise to verify the correctness, by replacing R and G
in (1) and (2) with the expressions for R and G in (3) and (4).

I believe there are methods in the marray packages for calculating R
and G from M and A like the above, but I don't know the exact name of
them.

BTW: I think it's better to ask these type of questions to the
Bioconductor (of which marrayNorm is part of) mailing list instead.

Best wishes

Henrik Bengtsson
Lund University, Sweden

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Binita Dutta
> Sent: den 22 januari 2004 13:47
> To: R-help at stat.math.ethz.ch
> Subject: [R] Calculation of normalised red and green intensities
> 
> 
> Dear Sir/Madam,
> 
> I could succesfully normalise my microarray data using 
> marrayNorm package. 
> However, i have not been able to get normalised red and green
channel 
> intensities through R package.  Is there a possibility to 
> write a formula 
> to calculate back the red and green channel intensities after 
> normalisation 
> of the data. Do I need to incorporate this formula in my R 
> script?  I am 
> biologist ans would seek your help to write this formula.
> 
> Thanking you,
> 
> Binita
> 
> 
> 
> Dr. Binita Dutta
> MicroArray Facility(MAF)
> UZ Gasthuisberg
> Onderwijs en Navorsing
> Herestraat 49
> 3000 Leuven
> Belgium
> 
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